The reason behind the move appears to be the Uruguayan government's decision to withdraw police protection at matches involving the country's big clubs Penarol and Nacional because of violence by their "barras bravas" hardcore fans.
"The well publicised acts that have occurred in recent times show the need for (the AUF board to take) a step to one side and allow other political views to govern our football," AUF president Sebastian Bauza's resignation letter said.
Leading newspapers El Pais and El Observador said on their websites (www.ovaciondigital.com.uy and www.elobservador.com.uy) that FIFA might interpret Uruguayan President Jose Mujica's decision as interference in football affairs and suspend the AUF and the Uruguay team from competition.
But Eugenio Figueredo, the president of South American football's governing body CONMEBOL, told Reuters that he knew of no FIFA investigation into the AUF.
Figueredo, a Uruguayan, said he did not believe there was any risk of 2010 semi-finalists Uruguay not playing at the World Cup in neighbouring Brazil that kicks off on June 12.
"I'm totally unaware (of this FIFA story). The truth is I have no news from CONMEBOL or FIFA," Figueredo said in a telephone interview from Chile where he was on a visit. "You can't draw conclusions from a rumour.
"When governments intervene, a national association is provisionally suspended (by FIFA)... But I have no proof the government played a part in Bauza's exit," added Figueredo, who heads the Paraguay-based CONMEBOL.
"The World Cup is already on top of us. Can you imagine a national association being suspended (now) for an internal or sports politics matter? FIFA is a bit more serious.
"I don't think Uruguay's place at the World Cup is at risk."
Mujica withdrew police protection after the latest violent incident when Nacional fans fought with police at the end of their team's 4-2 home defeat by Argentina's Newell's Old Boys in a Libertadores Cup match in Montevideo last Wednesday.
There were 40 arrests and several police officers and supporters were injured.
Bauza had differences with several club presidents over issues including television revenue from World Cup qualifiers and the AUF's reaction to Mujica's decision.
The government ruling led to the suspension of Penarol's first division match at Miramar Misiones at the weekend.
Uruguay, who boast the likes of Liverpool's Luis Suarez and Paris St Germain forward Edinson Cavani, are scheduled to play in Group D in Brazil alongside Italy, England and Costa Rica.
(Additional reporting and writing by Rex Gowar in Buenos Aires; editing by Mark Meadows)